OK, I'd have a solution now that produces the following (Duplex model as the test case):

    <layers>
        <IfcPresentationLayerAssignment id="#A-AREA-IDEN" Name="A-AREA-IDEN"/>
        <IfcPresentationLayerAssignment id="#A-CLNG-SUSP" Name="A-CLNG-SUSP"/>
        <IfcPresentationLayerAssignment id="#A-DOOR" Name="A-DOOR"/>
        <IfcPresentationLayerAssignment id="#A-FLOR-CASE" Name="A-FLOR-CASE"/>
        <IfcPresentationLayerAssignment id="#A-FLOR-HRAL" Name="A-FLOR-HRAL"/>
        <IfcPresentationLayerAssignment id="#A-FLOR-OTLN" Name="A-FLOR-OTLN"/>
        <IfcPresentationLayerAssignment id="#A-FLOR-STRS" Name="A-FLOR-STRS"/>
        <IfcPresentationLayerAssignment id="#A-GLAZ" Name="A-GLAZ"/>
        <IfcPresentationLayerAssignment id="#A-ROOF" Name="A-ROOF"/>
        <IfcPresentationLayerAssignment id="#A-WALL-MBNI" Name="A-WALL-MBNI"/>
        <IfcPresentationLayerAssignment id="#I-FURN" Name="I-FURN"/>
        <IfcPresentationLayerAssignment id="#S-BEAM" Name="S-BEAM"/>
        <IfcPresentationLayerAssignment id="#S-FNDN-FTNG" Name="S-FNDN-FTNG"/>
    </layers>
    <decomposition>
        <IfcProject id="1xS3BCk291UvhgP2a6eflL" Name="0001" LongName="Duplex Apartment" Phase="Project Status">
            <IfcSite id="1xS3BCk291UvhgP2a6eflN" Name="Default" ObjectType="" ObjectPlacement="1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1" CompositionType="ELEMENT" RefElevation="-0">
                <IfcBuilding id="1xS3BCk291UvhgP2a6eflK" ObjectPlacement="1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1" CompositionType="ELEMENT">
                    <IfcBuildingStorey id="1xS3BCk291UvhgP2dvNMKI" Name="Level 1" ObjectPlacement="1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1" CompositionType="ELEMENT" Elevation="0">
                        <IfcWallStandardCase id="2O2Fr$t4X7Zf8NOew3FNtn" Name="Basic Wall:Exterior - Brick on Block:138062" ObjectType="Basic Wall:Exterior - Brick on Block:130892" ObjectPlacement="1 0 0 0 0 1 0 0 0 0 1 0 -0 -0.2085 0 1" Tag="138062">
                            <IfcOpeningElement id="1xS3BCk291UvhgP2dvNrrP" Name="M_Fixed:4835mm x 2420mm:4835mm x 2420mm:145788:1" ObjectType="Opening" ObjectPlacement="1 0 0 0 0 1 0 0 0 0 1 0 3.548 -0.417 0.1 1">
                                <IfcPresentationLayerAssignment xlink:href="#A-WALL-MBNI"/>
                            </IfcOpeningElement>
                            <IfcOpeningElement id="1xS3BCk291UvhgP2dvN$je" Name="M_Single-Glass 1:0813 x 2420mm:0813 x 2420mm:171853:1" ObjectType="Opening" ObjectPlacement="1 0 0 0 0 1 0 0 0 0 1 0 2.63497 -0.417 0 1">
                                <IfcPresentationLayerAssignment xlink:href="#A-WALL-MBNI"/>
                            </IfcOpeningElement>

Uh oh!

Add layer information to IfcConvert's XML output? #141

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